O script de prólogo pode, na verdade, ser executado como qualquer usuário.
De man queue_conf
:
prolog
The executable path of a shell script that is started before execution of Grid Engine jobs with the same environment set- ting as that for the Grid Engine jobs to be started afterwards. An optional prefix "user@" specifies the user under which this procedure is to be started.
Portanto, definir prolog root@/path/to/prolog
deve tê-lo como root.